> -----Original Message-----
> From: Douali, Latifa
> Sent: Tuesday, July 12, 2005 4:26 PM
> To: 'amber.scripps.edu'
> Subject: RE: AMBER: TI - frcmod file
>
> Hi,
> I was running into the same problem. Therefore, I created 2 frcmod
> files. One for the unperturbed state and the other for the perturbed
> state containing dummy parameters. (I have new atom type in the
> unperturbed state). This procedure worked ok and I was able to create
> the .prmtop and the .inpcrd files. The prmtop file contains the force
> parmeters force constants.
> However, when I tried to perform other jobs (solvation and to create
> the prmtop and the inpcrd files for the solvated system). It gives
> again some warning that it does not recognize some parameters I have
> already in my frcmod file. So I see that the problem is not resolved.
> Here is my leap file.
> "
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Can't find angle parameter: DH - NB - CK
> Can't find angle parameter: DH - NB - CB
> Building proper torsion parameters.
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for NC-CB-CB-N*
> atoms are: N3 C5 C4 N9
> ** Warning: No sp2 improper torsion term for NA-C-CB-CB
> atoms are: N7 C6 C5 C4
> *** Improper torsion parameters missing ***
> atom names: H7-C8-N7-C5
> atom types: H-Cx-NA-CB =pert=> DH-CK-NB-CB
> Please add a dummy parameter of multiplicity 2
> for the pert types to your parameter set.
> - e.g. DH-CK-NB-CB 0.0 0. 2.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
> *** Improper torsion parameters missing ***
> atom names: N9-O8-C8-N7
> atom types: N*-O-Cx-NA =pert=> N*-H5-CK-NB
> Please add a dummy parameter of multiplicity 2
> for the non-pert types to your parameter set.
> - e.g. N*-O-Cx-NA 0.0 0. 2.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
> ** Warning: No sp2 improper torsion term for CT-Cx-N*-CB
> atoms are: C1' C8 N9 C4
> *** Improper torsion parameters missing ***
> atom names: C1'-C8-N9-C4
> atom types: CT-Cx-N*-CB =pert=> CT-CK-N*-CB
> Please add a dummy parameter of multiplicity 2
> for the non-pert types to your parameter set.
> - e.g. CT-Cx-N*-CB 0.0 0. 2.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
> total 7 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
> "
> Please advice
> Thank you
>
> Latifa
>
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
> Behalf Of Ilyas Yildirim
> Sent: Tuesday, July 12, 2005 3:07 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: TI - frcmod file
>
>
> Dear Oliver,
>
> I have checked out the ff03 parameters. The parameters for your system
> are defined in frcmod.ff03 and parm99.dat. Here are the parameters:
> - parm99.dat -
> CT-CT-C -N 1 0.100 0.0 -4.
> phi,psi,parm94
> CT-CT-C -N 1 0.07 0.0 2.
> phi,psi,parm94
> ---------------
> - frcmod.ff03 -
> CT-CT-C -N 1 0.0560 0.00 -3.
> CT-CT-C -N 1 0.0657 180.00 -2.
> CT-CT-C -N 1 0.7784 180.00 1.
>
> H0-CT-C -N 1 0.0110 0.00 -2.
> H0-CT-C -N 1 1.0607 180.00 1.
> ---------------
> First the parm99.dat is loaded and then the frcmod.ff03 is loaded. As
> far as I see, there are 5 torsional parameter defined for CT-CT-C -N.
> That means that if you do a perturbation from CT-CT-C -N --> H0-CT-C
> -N, you need to defined 5 torsional parameter for H0-CT-C -N, too. (If
> I am wrong, please someone correct me) The way I understood this
> particular error is, AMBER is doing the perturbation from one
> torsional parameter to another torsional parameters. As a result, we
> should define the same number of torsional parameters for both states.
> So, I would have put the following extra parameters in my frcmod.mod
> file:
>
> H0-CT-C -N 1 0.0 0.00 -4.
> H0-CT-C -N 1 0.0 0.00 -3.
> H0-CT-C -N 1 0.0 0.00 2.
>
> I would like to know what others think about this.
>
> Best,
>
> On Tue, 12 Jul 2005, Oliver Hucke wrote:
>
> > Dear All,
> >
> > I am setting up a TI simulation of the change of an ALA in a ligand
> > binding site of a protein to a GLY. The attached jpeg file shows the
>
> > changes of atom types I apply. In the process of preparing the
> frcmod
> > file for the atom type changes many errors of the following type
> > appeared when I tried to use my frcmod file with leap:
> >
> > --- from leap output ---
> > *** Proper torsion parameters missing ***
> > atom names: CB-CA-C-N
> > atom types: CT-CT-C-N =pert=> H0-CT-C-N
> > Please add a dummy parameter of multiplicity 1
> > for the pert types to your parameter set.
> > - e.g. H0-CT-C-N 1 0.0 0. 1.
> > (This is because multiple torsional potentials may apply to a single
>
> > torsion, and each is perturbed individually in gibbs.)
> > --- end of excerpt from leap output ---
> >
> > After doing what leap recommended, i.e. after adding all recommended
>
> > dummy torsions to my frcmod file, everything seems to be fine, i.e.
> I
> > am able to write the prmtop and crd output files with leap. (My
> frcmod
> > file that can be used with leap without problems is also attached).
> > BUT: some of the dummie torsions I had to add were actually "real"
> > torsions defined in the force field that I am using (ff03). For
> > example, leap asked me to add the following dummy torsion:
> >
> > H0-CT-C-N 1 0.0 0. 1.
> >
> > But in frcmod.03 I find:
> > H0-CT-C -N 1 0.0110 0.00 -2.
> > H0-CT-C -N 1 1.0607 180.00 1.
> >
> > Does using the dummy torsion in my frcmod file for the perturbation
> > not change these parameters defined in frcmod.ff03?
> >
> > Thank you very much,
> > Oliver
> >
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office)
> -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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Received on Wed Jul 13 2005 - 16:53:00 PDT
